Yeah it is a common issue with tracking the 6AT that the transmission actually overheats and goes into limp mode. As far as I know, there is no OTS bolt on AT cooler kit however I do know that Advan in Australia have made a custom AT cooler kit for an Australian member which used the LHS front intake duct, similar to an oil cooler.

Could you also retrofit the 6MT underbody panel?

In theory I guess that you could if they are the same size (which from memory they are) however if I also recall correctly, the 6AT pan is plastic and the underside of the 6MT is metal so I'm not sure how much the 6AT will benefit from the additional airflow.